The ship was originally around 116 feet (35 metres) long, making it quite capable of continental voyages. Although there were no initial plans to preserve the ship in its entirety, local people campaigned eagerly to ensure this. Initial estimates suggested that preservation would cost about £3.5 million and this sum was eventually found by the Welsh Assembly Government and Newport City Council. All of the ship's timbers have subsequently been raised and transferred to a dedicated industrial unit which the local council describes as "now the biggest wood conservation centre in the UK", where preservation and research continue. Due to its size, it has not been possible to display the ship in the basement of the new arts centre, as was originally proposed.

Artefacts found in the ship suggest that it was trading with Portugal in the fifteenth century. The abundance of artefacts linked with Portugal argues even that the ship was also built there. Dendrochronology has given a likely felling date of 1449 for the majority of the timbers and 1466 for some of the timbers used in its repair. Remnants of a cradle found beneath the ship suggested that it had been berthed for repair but then abandoned after the supports on the starboard side gave way.

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The excellent condition of the ship's timbers may possibly be due to the low oxygen level in the mud of the River Usk which has inhibited the presence of wood-boring creatures. Some time during its berth the port (left) side of the ship was cut down about 9 feet (2.7 metres) above the keel, but fortuitously this has preserved the correct shape of the hull. The starboard (right) side, which collapsed onto the river mud long ago, together with the ship's frames, has been preserved to almost its full height, although some planking has been distorted by the collapse.

The ship's dimensions have now been estimated at around 116 feet (35 metres) in length and around 27 feet (8.2 metres) in width. The vessel was clinker built with each plank overlapping the one below, the lower plank always being on the inside of the one above. The planks of the outer hull were positioned first and, on the Newport Ship, are secured to each other with iron nails driven through the overlap from the outside and then fitted with iron rove plates. The end of each nail was then hammered flat against the rove to produce a tight seal. Gaps along the overlap were secured by caulking with tar and animal hair. Hair from horse, cow, sheep and goat has all been identified in the Newport ship. The frames (ribs) of the ship were then fitted inside the hull and secured to the planks. Each framing piece was secured to the keel (spine) of the ship by having its keel cutout placed over the keel and held by precision of fit. Nails and trenails have not been used in this ship to secure frames to keel. The keel is made of beech, but the rest of the ship is made of oak, although no reason for this has yet been suggested. One possible explanation is a simple shortage of oak compared with beech at the time of construction. Almost all woodworking on the ship has been done using axes and adzes, with saw marks found on only a few timbers.

The inner hull of the ship is made up of stringers (large long planks that give the ship its longitudinal strength), providing a strong, smooth inner surface which probably supported the vanished cargo deck. The stringers were secured to the frames by trenails (cylindrical wooden dowels about 11⁄4 inches (3.2 cm) diameter and about 10 inches (25 cm) long) driven through pre-drilled holes in both timbers.

Cleaning of the timbers has led to the discovery, on the planking of the outer hull, of a series of marks deliberately scribed into the timbers. These appear to be either individual shipwrights' marks or instructions for the positioning of planks or fastenings. The conservation team is hoping that a pattern will emerge as the recording process continues. During the summer of 2007, the cleaning of barrel-top fragments revealed merchant marks. Some of these may resemble known marks of merchants from the city of Bristol, but this is not proof that they originated there.

Initial dendrochronology on certain specimen timbers produced a date of 1465 – 1466, but further research has revealed that the timbers originate from the Basque Country of northern Spain dating from 1449. The discovery in the spring of 2006 of a French "petit blanc" (small white) silver coin inserted into a cut out in the stempost/keel join was a major step forward. Placed, perhaps, as a token of good fortune at the start of the ship's construction, this coin was minted in Crémieu in the Dauphinois region of France between May and July 1447. So the ship could not have been built before this date. Similarly, the tree trunks found under the hull and forming the support for the ship when under repair, have a dendrochronology date of 1468 – 1469.[1] Very provisionally, this would give the ship a maximum working life span of c. 25 years.

There is circumstantial evidence that by 1469 the ship may have belonged to and been under repair for the Earl of Warwick (Warwick the Kingmaker). A letter of authorisation dated 22 November 1469 from Warwick to Thomas Throkmorton, his receiver of Glamorgan and Morgannwg, authorised various payments for "the making of the ship at Newport" which could be construed as repairs to the badly damaged vessel.[2][3] Newport was such an insignificant port at this time that it seems highly unlikely that such a large trading vessel would ever have come to the town unless for emergency repair.

Severe (but ancient) damage to the mast-step of the ship may be the reason why the vessel was brought into Newport for repair. Why the ship was then abandoned is still unknown.

During excavation several hundred objects were found within the ship, ranging from a stone cannonball to grape seeds and including a damaged hour glass, 13 single shoes of which one is a very expensive shoe, pieces of cork and some Portuguese coins.[4] The seeds, cork and coins would suggest trade to and from the Iberian peninsula and the presence of Merino sheep wool in the caulking material supports this idea; but is not conclusive proof. Members of the Albaola Society based Pasaia, near Bilbao in the Basque region of Spain, after studying the ship's structural details believe that the ship may have been built by Basque shipwrights, either in the Basque region of Spain or south-western France.

The first stage of the restoration project; the cleaning and recording of the timbers, was completed in April 2008. The timbers were immersed in ordinary mains water, in a series of large shallow tanks. Small fish, including domestic goldfish and a sturgeon were successfully used to predate the various marine invertebrates that were coincidentally collected when the timbers were salvaged.

The next stage, the conservation of the timbers, which began later in 2008, involved immersing the timbers in polyethylene glycol (PEG) solution for an extended period. Before this began, some of the timbers required treatment with triammonium citrate to remove residual iron residues in the nail holes of the outer hull planking. This unexpected additional phase added no more than between fifteen and eighteen months to the project.

As of September 2016 all of the ship's timbers have completed their PEG treatment cycle and are now being freeze dried to draw out all of the residual water in preparation for the eventual reconstruction of the vessel.

A conference entitled 'The World of the Newport Ship' was held at the University of Bristol on 17–18 July 2014, examining the vessel, her significance and her historical context.[5] The conference papers are likely to be available in late spring 2017.

The Friends of Newport Ship organises regular open days when the project may be viewed in its current state of restoration along with exhibits to explain the restoration process. Visitors have the opportunity to talk to members of the ship team, and find out about the excavation and the campaign to save the ship, through tours of the facility run by the support group Friends of the Newport Ship. Generally the Ship Centre is open every Friday and Saturday between Easter and the end of October, and from on Saturdays only from spring half term until Easter and for November and early December.[6]